Uncovering Origins
by fanfictionated
Summary: Skyward Fanfiction. Skye is caught up in a mission involving her roots. What happens when she's captured by someone of her past? What really happened when she was dropped at St. Agnes, and why? What will she find out while the team is working to find her? Or will they think she just abandoned them again?
1. Chapter 1

Disclaimer: Sadly, I don't own agents of shield :(

**A/N:** Hi! This is a skyward fanfiction cause I'm crazy about them, they would be so cute together :3 This is my first fanfic so please don't be to harsh. I hope it's not bad, good reading :) italics are thoughts, characters might be a little ooc.

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_Chapter 1_

I woke up to the sound of my alarm clock, such a horrible sound to wake up to! It kept ringing with that awful strident irritating sound. I turned on my belly and covered my ears with the pillow whist groaning. As the annoying sound continued, I began to wake up and my head started to clear. _I have to be on the cargo bay for practice at 7:30. _I sighed and checked the time. 7:20. _Shit, I only have 20 minutes to get ready. _I jumped out of bed, almost hitting my head in the wall, I keep forgetting I'm on a plane.

I brushed my teeth and got dressed the fastest I could. Then I ran to the cargo bay only stopping at the kitchen to eat a cracker I stole from Fitz's hand, leaving him behind grumbling.

I reached the cargo bay where Ward was sitting at a mattress looking bored.

"Sorry I'm late" I said slowly evaluating his reaction

"Then why are you still standing there? Do ten push ups" He said. At least it wasn't that bad of a punishment, pull ups are worst.

I did the push ups and then we started the training with pull ups, chin ups and running in the treadmill. Lastly, he started teaching me the basics of hand to hand combat and after 20 minutes of that, we stopped.

I went to take a shower. I never had training lessons like this before, in the first days, I got so many cramps I refused to get out of bed till midday, when I got really hungry.

After I showered, I went to fitzsimmons who were playing scrabble sitting in the couches. I joined in, but soon started to lose. They were really good, probably because they're scientists with an IQ that doubles mine.

After approximately 1 hour later, may came in and told us we got a case. We joined in the briefing room listening to Coulson as he told us we were going to Russia to find a rogue agent that had been sighted there.

I was going in on the field in a van with FitsSimmons in case backup was needed and also to help to keep an eye on them while they completed the mission. I was feeling nervous, what was odd, even Ward had to admit that. I never fell nervous, though there was something about this that i couldn't get out of my head. I could practically smell danger from this mission. When Coulson showed a picture of the agent. My first reaction was shock, but i disguised it.

One of the thing I was good at was disguise, I needed a lot of that while growing up on foster homes, you were never safe. I will probably be a kick ass agent when it'll come to working undercover. Not only am I a good liar, I have a good ability to manipulate people and even making my mind comply with what I want to assume truth at the moment. Very good ability to have when it comes to polygraph tests. Not that I ever took one... And I wasn't playing my team, it's the first time I ever felt accepted in a group, they kind of are my family now. Why would I want to mess this up?

The rogue agent was still in my mind. I swear i can recognize his face from somewhere and not somewhere normal like the mall or the street. I knew it was something else. I'll try to find out when he has his ass beaten up by May and is locked down ion the plane.

The plane was already recovered from the damage of last Tuesday, from when Tobias decided to cut the power wires because he thought we were going to hurt his crush.

The next day we landed on a clearing and after opening the cargo doors headed into the city in a white van.

Fitz was nervous as always, Simmons fascinated with the view, May with her typical 'Don't mess with me' look at the steering wheel and Ward was sitting next to me studying his new 'night-night' pistol model, as Fitz liked to call it. Coulson had stayed at the plane with some local agents that were filling him in with the details of the hunt.

I was looking at Ward when he removed his attention from the pistol to look at me.

"What?" He asked with a furrowed eyebrow.

"Nothing, just trying to figure out if the robot has emotions." I said casually with my ear to ear typical skye smile.

" I'm not a robot." He replayed groaning.

_Ohhhhhh, that was cute. Wait, go back just a second! Did I say cute? No way, This Ward, Skye! Wake up, you live to annoy the hell out of him, not thinking he's cute, though he is... agrh! I'm gonna stop now._

"Sooo... Does anybody want to play a game?" I suggested to lighten the mood.

" Yeah good idea! Let's play I spy!" Said Jemma enthusiastically, Fitz fallowing right behind

" yeah!"

"No, please don't" Ward said. He wasn't in the mood for games at the moment, especially because he was sitting next to skye and it took more self control than he expected to sit next to her. He didn't know where that came from. He was with Skye every day of the week but lately he was feeling different towards her. _For God's sake. That girl lives to annoy you! What's going on? _He thought.

"Come one Ward, play too!" Said Simmons expectant.

"Fine..." He said giving up.

" I start! I spy with my little eye something...red" Fitz said.

They played this game for twenty minutes with Grant giving random guesses when the team required his participation until they arrived at the city.

They stopped in a quiet road with few people where Ward and May got out and placed their mics. We turned on the computer and watched them going in the bar with the mob connected to the rogue agent. It was going smooth until suddenly all the screens went black.

" What the bloody hell?" Fitzsimmons said at the same time.

Some noise came from outside the van making us go silent. Fitzsimmons turned to me with wide eyes expecting me to do something. Right... I was the back up, and I'm screwed.

Gathering some courage I grabbed a pistol and opened the doors stepping outside. My hands shakily held the pistol while I looked around trying to find the source of the noise. I waited a few seconds while holding my breath to see if i heard someone. When everything was quiet once more I started to outline the truck.

I noticed something shiny in the ground. I furrowed my brow and took slow steps near it. When I was looking down at it I gasped, it couldn't be. I fell to the ground, picking up the locket. With bulging eyes I inspected the locked and found the engraving on the side of the cross. '_**Skye**__**1990'**__._ It was her locket! The only thing the nuns found her with as a baby. How was this possible? It had been in a fire on one of the foster homes she was in and was never recovered.

I was stunned looking at the locket, so I didn't hear when quiet steps sounded behind me. The last thing I recalled before passing out, was a jolt of electricity in my neck that made my hole body shake and fall to the ground, numb.

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**A/N: **Let me know if I should continue this story and please review, I love reviews! :D


	2. Chapter 2

**Disclaimer:** Unfortunately, I do not own agents of shield :(

**A/N: **I'm so sorry for taking so long to update. My computer got broken and went to be repaired, so I couldn't update. On a happier note, I can't believe the amount of reviews I got! Thank you all so much! As I previously said, this is my first fanfiction and I'm not native English so please forgive any misspellings or mistakes in grammar that I might commit. Enjoy your reading!

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_Previously:  
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_I noticed something shiny in the ground. I furrowed my brow and took slow steps near it. When I was looking down at it I gasped, it couldn't be. I fell to the ground, picking up the locket. With bulging eyes I inspected the locked and found the engraving on the side of the cross. '__**Skye1990'**__. It was her locket! The only thing the nuns found her with as a baby. How was this possible? It had been in a fire on one of the foster homes she was in and was never recovered._

_I was stunned looking at the locket, so I didn't hear when quiet steps sounded behind me. The last thing I recalled before passing out, was a jolt of electricity in my neck that made my hole body shake and fall to the ground, numb._

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_Chapter 2_

Fitzsimmons waited in the van, shaking like a leaf, trying to make sense of what was happening. Everything had happened so fast, it was like the hole thing was a blur. Skye had exited the van, with a pistol in her shaking hands, Simmons felt so much compassion and gratitude towards her. Skye was surely as scared as them, she hesitated in the ground outside and proceeded to close the doors. Then they heard what they assumed was her outlining the van, followed by a weird sound like a jolt of electricity and a thud. Fitzsimmons blood ran cold by then.

They exchanged worried looks, and looked at the double doors. They were sure something bad had happened, what if Skye was hurt?

Simmons was shaking in fear, what could have happened to Skye? Coulson shouldn't had sent her as backup, she couldn't even distinguish the magazine release from the trigger! What if someone caught her? She was still learning, she a rookie as agent Ward liked to call her. He obviously harbored feelings towards the hacker.

"Fitz, I think we should check on Skye. She may be in trouble." Simmons said worriedly, lately she had begun to care for Skye as a good friend, maybe even a best friend. She never had one before, so she very much cared for her.

"Yeah, I'll go, stay here and call Coulson. Let him know what's going on." Fitz told her hurriedly stuttering, he too was nervous and afraid.

"Okay, be careful" Simmons said in her British accent. She wanted to go along but she knew someone had to warn Coulson about the current situation, they might be in big trouble.

Fitz gathered the courage he could and opened the doors slowly, by this point he was shaking so much he could barely keep them still. But, for once, he had to prove himself. He couldn't when Ward took his parachute to jump for Jemma but now he could, this was his chance. He jumped out of the van and looked around for any sign of movement. Nothing was in sight, just trees and a lonely road, and at the other side of the road, the bar where May and Ward were at the moment, not fighting, he hoped.

He outlined the truck hoping to see Skye but she wasn't in sight, nor her captor, if there was a captor. He had to face every possibility, even the bad ones.

"Skye!" He yelled out to the woods yet had no response. He ran to the truck and got inside.

"Fitz?" Simmons asked, hoping to she Skye enter the van after Fitz, making a joke and looking joyous.

"She isn't here, I really think we should get Ward and May out of the bar. Have you called Coulson?"

"I'm trying, there's not much of a reception out here. She isn't here? How can that be possible she just left!"

"I don't kn...Look there's May and Ward."

May and Ward were exiting the bar and running towards the van. As they got closer, Ward started making signs trying to tell them to start the engine. Simmons figured it out faster than Fitz and hopped to the front rotating the key leaving Fitz with a " Wha?". Simmons jumped to back again as May and Ward entered the vehicle.

"Step on the gas!" Ward told to may, more like yelled, as she got in the driver's seat.

"Buckle up." May told Fitzsimmons as she hit the accelerator causing the van to shake as it started to move at full speed.

Fitzsimmons ran to their sits trying to keep balance as they swung, colliding once as they tried to sit down. Eventually they did and fastened their seat belts.

"What happened in there?" Fitz asked with bulging eyes after seeing the building May and Ward were just in blow up to pieces.

"We figured something was wrong when we lost contact with you, and then we heard the tick tack of a bomb... The rest you can figure out by yourselves" May said

"Luckily it was a clock bomb. Hey! Where's Skye?" Ward asked looking behind and not seeing Skye, he was sure his heart just skipped a beat.

"She disappeared right before you came in the van. She vanished!" Fitz said, eyes widening. In the heat of the moment he forgot to tell them the hacker was missing.

"What? How? How could you not tell us this? Are you crazy?" Ward suddenly yelled. He felt like his blood was boiling in his veins. His rookie was missing!

"I couldn't! You burst in here demanding full speed I didn't get the chance to warn you! My mind just went blank." Fitz yelled back trying to defend himself against Ward's rage.

Simmons, predicting a yelling match between Ward and Fitz as it would probably lead to punches, decided to intervene.

"Hey guys, stop it! Yelling won't fix anything, in fact I'm sure it will only make it worst! We were in the van, monitoring you and then all the screens went black! We heard some noise outside and Skye went to check it out, after we stopped hearing footsteps everything went quiet so Fitz went to figure out what was going on while I was trying to call Coulson. Fitz returned a few minutes later with no Skye and you two came bursting in after that. We didn't have any time to warn you! This is nobody's fault! She just... vanished." She finished already with short breath

"We have to find her! May turn around" Ward ordered already taking command.

"First we have to warn Coulson to what is going on. I'll drive to the nearest city, once we're there, we'll wait for backup and then we will go looking for Skye" Said May rolling her eyes and putting emphasis on the 'when'.

"Fine... drive faster" Ward commanded.

Ward was used to being in charge, he liked to have the advantage, the information. It was the way he coped with a childhood of following orders and being mistreated. It was the way he found to deflect the wrath he felt towards his brother to the well of the community, by killing the bad guys and tearing the truth out of them so he could put more bad guys away.

May seemed nonchalant and uninterested as always but deep down she was as scared for Skye as Fitsimmons. Skye was always bright and shiny, and nothing should chance that, she had been like that once, but that had been taken away from her. She didn't want the same thing to happen to the happy and carefree hacker, though if she wanted to be a Shield field Agent she was going to need to chance her style of living. She couldn't be gullible or eager for acceptance, she had to deal better with rejection and keep tough, not act. Acting would not save in case of capture where one of the bright scenarios would be torture.

Ward was being eaten alive by concern as he tried to get his mind of his rookie. _His rookie._ He was supposed to always be protecting her. Had she just walked away? He didn't even want to ponder on that idea. But it could be true, She had proved to be not reliable in the past, who says the same thing didn't happen again? The way he felt after the betrayal, he never wanted to feel like that again. He had let her in, even relied on her, enough to tell her about his past. He didn't want to feel that way again, so when she offered support after the whole staff incident, he had turned her down and went to may even though he really wanted to be with Skye deep down. Now, all he wanted to focus on, was finding her, even if they had to lock her away.

" I'm a bit peckish, can we stop at that bakery?" Fitz asked breaking the silence

AoS-AoS-AoS-AoS

Skye regained conscience bit by bit. Her head hurt like hell and she felt like she had been ran over by a bus. Her eyelids were more heavy than usual so it took and extra effort to open her eyes. When she finally did she took a look around but couldn't see a thing, everything was dark. For a moment she was scared her kidnapped blinded her but then she felt pressure around her eyes and realized they were covered by some fabric. She was in movement, the place where she was in was in movement, that is. She could feel the ground shaking and the sensation reminded her the one of travelling by car. She must be in a trunk. It's a wide space, she could roll around.

The truck, she assumed, took a lot of turns in which she rolled around hitting boxes that were lying around and also the walls of the vehicle. Her hand were tied behind her back and her feet were tied to. Her hole body still hurt from the tazer that her attacker used to paralyze her outside the van were they were. Oh my god! Was the rest of the team ok? She seemed to be alone, she tried to mumble something bit there was a fabric blocking her mouth.

Now fear was starting to take over, where were her kidnappers taking her? Were they going to hurt her? What if they wanted to know something? She didn't hold any valuable information but still, they could think she did.

After what seemed to be an hour and a half of freaking out and self questioning, the truck came to a stop and Skye heard movement.

She interpreted the noise as steps and her suspicions were proved right as the sound came closer and stopped behind her.

Then the trunk was open and the blindfold taken off and for a minute she was blinded by the sudden light, but then she saw him...

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**A/N: **Hope you enjoyed :) Please don't forget to review!


	3. Chapter 3

**Disclaimer: **Trust me, if I owned agents of S.H.I.E.L.D you'd know by now ;)

**A/N**: Because I took so long to update last time, here's the next chapter :) Sorry for any mistakes that you may or may not find and thank you all super much for all off your reviews :D Enjoy.

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_Previously:_

_After what seemed to be an hour and a half of freaking out and self questioning, the truck came to a stop and Skye heard movement._

_She interpreted the noise as steps and her suspicions were proved right as the sound came closer and stopped behind her._

_Then the truck was open and the blindfold taken off and for a minute she was blinded by the sudden light, but then she saw him._

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_Chapter 3_

She couldn't believe who she saw before her eyes. It really was him,after all these years, Elias Benesch. She almost didn't recognize him, but after a minute of staring at him completely dumbfounded, she had to face it. The similarities were there, his face was a little aged but other than that he was the same. She only hoped that that didn't apply to his personality.

He was one of her foster parents along with his wife Clarissa, they were the worst she ever had. It all went down when she was 11 years old, her own personal hell.

He was drunk all the time, not very different from all the foster parents she had and the couple only adopted her for the money they got from the government for sheltering her, if you could call that sheltering. That was a time she opted to forget.

The yelling and the beating... Not only for her, he often got mad at his wife. He constantly drank, his eyes were bloodshot and evil, sometimes she swore she could see complete blankness of feelings and only darkness emanated from them. They were electric blue, the colour of death.

Once he went almost completely savage, he came a her with a kitchen sharp knife he grabbed from Clarissa's hands when she was trying to defend herself against his wrath but she ran to the forest, where she spent the night. Her last night with the Benesch Family, and the last time she saw them ever.

She went to the tree house on top the hill were she used to meet her best friend Dannie, short for Daniela, she had portuguese origins. Skye still kept a mental image of her because, unfortunately, she had no photos. Dannie had long black air with natural red highlights that hand loose most of the time but was sometimes braided, dark chocolate eyes and white teeth. Her personality was the exact opposite of Skye, she was as quiet as she could and only let her guard down with Skye.

_Flashback_:

_ She was terrified. Feeling small standing against the tall scary evil man that burst into her room with a big knife, Skye was temporarily paralyzed with fear and grabbed the thin covers from her cheap uncomfortable bed._

_ She contemplated the drunken man that swung by the door jamb pointing the knife shakily at her small shrunken terrified form on the bed that clung for dear life to the unwashed bed sheets. She looked at her small hands and jumped out of bed running to the window overturning the small bedside lamp as she climbed on top of the bedside table and tremblingly opened the window and jumped outside to the darkness of the cold night. _

_ He had made his way to the window trying to move fast and was able to catch her left foot with is hands before she could be out of the bedroom completely. She screamed and cried kicking with her feet for him to let her go. The knife was plunged into her foot and she kicked him in the nose as a piercing cry of pain perforated the otherwise silent night. He released his grip on her due to the sudden kick. Surprised, he brought his hand to his nose and it came back stained with blood this caused him to growl into the night as Skye ran away barefoot._

_As soon as she reached the ground outside she got up and ran through the night, never stopping and never looking back. As she was in the edge of the treeline she heard a growl coming from the house behind her that she'd just abandoned._

_She ran over the rubble that clung to her already hurt feet and painfully pierced her skin. She kept running despite the pain and the occasional branches that lied on the ground, she was driven by fear. Skye panted and could barely stand when she reached her goal. She grabbed the trees she so joyously climbed up days before with the promise of fun. When the little girl was on the top, she entered the tree house backed up against a wall crawling and sat there hugging her knees and crying. She stayed quiet all night, hearing wolves howling and groaning and fighting about the carcass of a dead animal. She just stayed quiet and motionless. That's how they found her the day after._

_A lumberjack found her, he followed the blood trail she left the night before due to her injured foot and was surprised to find the terrified little girl in the corner of the tree house hugging her knees swinging back and forth. she was painting and her eyes were wide though she showed no signs of acknowledging him even when he tried to talk to her. Her eyes seemed glazed and were centered in a point somewhere in her sight, only visible to her. The adrenaline she felt the night before was long gone and she was feeling week and soiled._

_Skye tried to fight him off as he carried her down and took her to the hospital. There they did all sorts of tests and concluded that she was traumatized, and suffered negligence and maltreatment. She stayed in the hospital for a few days and was later sent off to St Agnes were she was assigned to countless psychiatrists._

She tried to forget her past over the years, even deleted it from the files of agencies like SHIELD so she wouldn't have to face it. But she still needed answers to questions she never stopped asking. She was still carrying on the never ending quest to find her parents. Skye needed the truth, needed to be free. She hated moments when she was helpless and worthless.

She stared at her nightmare and refused to cave in and submit herself so she kept her chin up and prise in her eyes.

"I thought you were dead" she said with a challenging glow in her eyes.

"You tought wrong. I faked my death, not that hard. But Clarissa died, yeah, I had enough of her, she was really annoying. I burned down the whole house and left her in there, but you got away, not a mistake that I'll repeat." He said with a smirk with an evil glint in his eyes.

"Just wait until my team gets here and then you'll wish you were dead for real" She replied

He slapped her and threw her in his shoulder. He carried her inside the warehouse and placed her in a chair.

" Now you'll stay here until the bad men arrive and you will not make a sound, get it?" He told her while tying her to the chair.

" Actually... No" she said sarcastically

" I see you haven't lost your sense of humor, it's a shame that it won't save you now." He snapped back

He then smiling picked up the gag and covered her mouth with it. She watched him walk away and close the door. As soon as he was out of her sight she tried to get the gag and the ties off. She was able to loosen the grip of the gag but did the exact opposite on the rope tying her hands and feet.

She stayed like that for about an hour when three men entered the building and walked towards her. They picked her up despite her muffled protests and carried her out. They tossed her in a trunk and left her in the dark. Again.

AoS-AoS-AoS-AoS-AoS

FitzSimmons sat in the couches of the hotel were the team had checked in trying to figure out what had happened to Skye while Ward sat the bar sipping bits of his drink trying to forget about his rookie.

When they reached the nearest city May went to a payphone and called Coulson. Coulson told them to go to a clearing in the middle of the forest where they headed to after the call. Whitin minutes the S.H.I.E.L.D plane emerged from the sky. Coulson brought more agents to search for Skye and that's what they did for the rest of the day.

The only thing found was discovered by Ward and was a tiny cross with an engraving on the side saying **Skye1990**. He kept it and was now holding it in his hand looking at it.

Nick Fury was certain that she had run away in her own feet and made sure that Coulson knew of his suspicions. Like he pointed out, there were no signs that Skye had been captured, no blood, no tire marks in the ground, no footsteps, no explosion on the other side of the road didn't help much either. It seemed as if she just vanished, so Fury just assumed she ran away and told Coulson how he knew an waned him that the hacker was going to be trouble for S.H.I.E.L.D. The other agents that were brought in to look for Skye all thought she ran and tat she planted the bomb herself and led them there so she could escape.

Even Ward was starting to think that maybe Skye had run away. What made him grumpy to anyone that spent at least a second around him to hear him grumble. He was mad, mad at Skye for running and mad himself for letting this happen. When he got inside the bar with May he should of known something was off the second he set a foot inside the building, there was no one there except the bartender and the local drunks. When they realized there was a bomb they made them get out, they ran off the back door and May was trying to deactivate the bomb but when there were 30 seconds left they ran out of the place and got inside the van.

The first thing FitzSimmons came up with was tracing the feed from the location back to her but when they couldn't they concluded that either she was underground, had taken out te bracelet or was in someplace that was blocking it.

Simmons still hadn't slept and Fitz was trying to convince her to get some sleep and eat something, though he himself didn't waste a waking moment, trying to figure out ways to find Skye.

AoS-AoS-AoS-AoS-AoS

Skye had spent the whole day rolling and being carried around and she'd had enough of it. She had been moved from car to car, trunk to trunk always with the blindfold and gag on because of the sarcastic remarks and spitting in one of the men once, that earned her a slap that made her cheek red and tingling. She still felt the spot sting. The car where he was currently in abruptly stopped making her hit the wall of the trunk and she grunted in response.

One man opened the trunk and threw her over his shower like a sack of potatoes. At first she protested by grunting and kicking him but he punched her at that. Then,he carried her and stopped after a while. She was dropped in a chair and the blindfold and gag taken off. Finally! Now she only had to annoy them to death... shouldn't be that hard according to Ward.

The three guys left her there and went away. _Not again! I had enough of being dropped nd picked up today! _She thought to herself starting for the first time, since Elias captured her, to become angry, before she was only scared and terrified if you must call it that, but now rage was starting to build up inside of her.

"Can't you stop this already? I've had enough! Stop playing games, stop the suspense! Who are you what do you want?"She yelled out to whom was close enough to hear her.

The old rusty room that contained her had dust every where and she could her the bickering of mice. Then the old big door right in front of her opened squeaking and making piles of dust fly through the air. She coughed and squinted her eyes attempting to see the figure standing at the door.

After some seconds that seemed like hours the dust in the air subsided and her eyes adapted to the light finally identifying the figure standing serious by the door. It was him, the rogue agent. And Skye was sure he held the answers to all her questions.

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**A/N: **Hope you enjoyed :) Please review and tell me your opinions


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